replace tabs and remove trailing whitespace in lib folder with updated script
This commit is contained in:
Axel Kohlmeyer
@ -66,12 +66,12 @@ namespace ATC {
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/** Predictor phase, executed before Verlet */
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virtual void pre_init_integrate() {
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feEngine_->partition_mesh();
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feEngine_->partition_mesh();
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update_step();
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};
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/** Predictor phase, Verlet first step for velocity and position */
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virtual void init_integrate();
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virtual void init_integrate();
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/** Predictor phase, executed after Verlet */
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virtual void post_init_integrate();
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@ -127,7 +127,7 @@ namespace ATC {
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/** access to interscale manager */
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InterscaleManager & interscale_manager() {return interscaleManager_;};
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/** access to lammps interface */
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LammpsInterface const * lammps_interface() const {return lammpsInterface_;};
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/** access to time filter */
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TimeFilterManager * time_filter_manager() {return &timeFilterManager_;};
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@ -142,7 +142,7 @@ namespace ATC {
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/** compute vector for output */
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virtual double compute_vector(int /* n */) {return 0.;}
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/** compute vector for output */
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virtual double compute_array(int /* irow */, int /* icol */) {return 0.;};
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virtual double compute_array(int /* irow */, int /* icol */) {return 0.;};
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int scalar_flag() const {return scalarFlag_;}
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int vector_flag() const {return vectorFlag_;}
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int size_vector() const {return sizeVector_;}
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@ -164,16 +164,16 @@ namespace ATC {
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/** time/step functions */
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bool sample_now(void) const
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{
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{
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int s = step();
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bool now = ( (sampleFrequency_ > 0) && (s % sampleFrequency_ == 0));
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return now;
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}
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bool output_now(void) const
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{
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{
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int s = step();
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bool now = ( (outputFrequency_ > 0) && (s == 1 || s % outputFrequency_ == 0) );
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bool now = ( (outputFrequency_ > 0) && (s == 1 || s % outputFrequency_ == 0) );
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now = now || outputNow_;
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return now;
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}
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@ -328,7 +328,7 @@ namespace ATC {
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const std::map<std::string,std::pair<MolSize,int> > & molecule_ids() const {return moleculeIds_;};
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/** access to internal element set */
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const std::string & internal_element_set() {return internalElementSet_;};
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//----------------------------------------------------------------
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/** \name mass matrix operations */
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@ -339,7 +339,7 @@ namespace ATC {
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// inverted using GMRES
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void apply_inverse_mass_matrix(MATRIX & data, FieldName thisField)
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{
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if (useConsistentMassMatrix_(thisField)) {
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//data = consistentMassInverse_*data;
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data = (consistentMassMatsInv_[thisField].quantity())*data;
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@ -351,7 +351,7 @@ namespace ATC {
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void apply_inverse_mass_matrix(const MATRIX & data_in, MATRIX & data_out,
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FieldName thisField)
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{
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if (useConsistentMassMatrix_(thisField)) {
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if (useConsistentMassMatrix_(thisField)) {
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//data_out = consistentMassInverse_*data_in;
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data_out = (consistentMassMatsInv_[thisField].quantity())*data_in;
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return;
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@ -365,7 +365,7 @@ namespace ATC {
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DIAG_MAN &mass_mat(FieldName thisField)
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{ return massMats_[thisField];};
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//---------------------------------------------------------------
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/** \name mass matrices */
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@ -383,13 +383,13 @@ namespace ATC {
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void register_mass_matrix_dependency(DependencyManager * dependent,
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FieldName thisField)
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{
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if (useConsistentMassMatrix_(thisField)) {
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if (useConsistentMassMatrix_(thisField)) {
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consistentMassMatsInv_[thisField].register_dependence(dependent);
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return;
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}
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massMatsInv_[thisField].register_dependence(dependent);
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};
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void apply_inverse_md_mass_matrix(MATRIX & data, FieldName thisField)
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{ data = (massMatsMdInv_[thisField].quantity())*data; };
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void register_md_mass_matrix_dependency(DependencyManager * dependent,
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@ -416,11 +416,11 @@ namespace ATC {
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return man->second;
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};
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/*@}*/
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//----------------------------------------------------------------
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/** \name Interscale operators */
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//----------------------------------------------------------------
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bool use_md_mass_normalization() const { return mdMassNormalization_;}
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bool use_md_mass_normalization() const { return mdMassNormalization_;}
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bool kernel_based() { return kernelBased_; }
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bool kernel_on_the_fly() const { return kernelOnTheFly_;}
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bool has_kernel_function() { return kernelFunction_ != nullptr; }
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@ -439,20 +439,20 @@ namespace ATC {
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double ke_scale() { return keScale_; }
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double pe_scale() { return peScale_; }
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/** from a atom group, find the nodes that have non-zero shape function contributions */
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bool nodal_influence(const int groupbit, std::set<int>& nset, std::set<int>& aset, double tol =1.e-8);
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int nodal_influence(const int groupbit, std::set<int>& nset, std::set<int>& aset,
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int nodal_influence(const int groupbit, std::set<int>& nset, std::set<int>& aset,
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bool ghost,
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double tol =1.e-8);
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/*@{*/
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/** Restrict based on atomic volume integration for volumetric quantities : given w_\alpha, w_I = \sum_\alpha N_{I\alpha} w_\alpha */
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void restrict_volumetric_quantity(const MATRIX &atomData,
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MATRIX &nodeData);
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MATRIX &nodeData);
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void restrict_volumetric_quantity(const MATRIX &atomData,
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MATRIX &nodeData,
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const SPAR_MAT & shpFcn);
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@ -474,7 +474,7 @@ namespace ATC {
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protected: /** methods */
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/** time functions */
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void set_time(double t=0) {simTime_=t;};
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void update_time(double alpha = 1.0)
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void update_time(double alpha = 1.0)
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{
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double dt = lammpsInterface_->dt();
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simTime_ += alpha*dt;
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@ -506,7 +506,7 @@ namespace ATC {
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virtual void read_restart_data(std::string fileName_, RESTART_LIST & data);
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virtual void write_restart_data(std::string fileName_, RESTART_LIST & data);
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void pack_fields(RESTART_LIST & data);
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void pack_fields(RESTART_LIST & data);
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/** mass matrices */
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DIAG_MAT massMatInv_;
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@ -564,11 +564,11 @@ namespace ATC {
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void reset_fields();
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private: /** methods */
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private: /** methods */
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ATC_Method(); // do not define
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protected: /** data */
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/* parsed input requires changes */
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bool needReset_;
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@ -609,7 +609,7 @@ namespace ATC {
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PerAtomQuantity<double> * atomProcGhostCoarseGrainingPositions_;
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PerAtomQuantity<double> * atomReferencePositions_;
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/** number of unique FE nodes */
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int nNodes_;
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@ -631,17 +631,17 @@ namespace ATC {
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bool trackDisplacement_;
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/** map from reference positions to element id, pointer is to internal only */
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bool needsAtomToElementMap_;
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PerAtomQuantity<int> * atomElement_;
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PerAtomQuantity<int> * atomGhostElement_;
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/* use element sets to define internal and/or ghost regions */
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std::string internalElementSet_;
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/** atomic ATC material tag */
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double Xprd_,Yprd_,Zprd_; // lengths of periodic box in reference frame
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double XY_,YZ_,XZ_;
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double boxXlo_,boxXhi_; // lo/hi bounds of periodic box in reference frame
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@ -671,22 +671,22 @@ namespace ATC {
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/** base name for output files */
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std::string outputPrefix_;
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/** output flag */
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/** output flag */
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bool outputNow_;
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/** output time or step (for lammps compatibility) */
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bool outputTime_;
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/** output frequency */
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int outputFrequency_;
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/** sample frequency */
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int sampleFrequency_;
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/** sample counter */
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int sampleCounter_;
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TAG_FIELDS filteredData_;
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TAG_FIELDS filteredData_;
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double peScale_,keScale_;
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@ -702,7 +702,7 @@ namespace ATC {
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int sizeVector_; // N = size of global vector
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int scalarVectorFreq_; // frequency compute s/v data is available at
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int sizePerAtomCols_; // N = size of per atom vector to dump
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double **perAtomOutput_; // per atom data
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double **&perAtomArray_; // per atom data
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int extScalar_; // 0/1 if scalar is intensive/extensive
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@ -724,15 +724,15 @@ namespace ATC {
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/** \name time integration and filtering fields */
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//---------------------------------------------------------------
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/*@{*/
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FIELDS dot_fields_;
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FIELDS dot_fields_;
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FIELDS ddot_fields_;
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FIELDS dddot_fields_;
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/** Restricted Fields */
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FIELDS nodalAtomicFields_; // replaces fieldNdFiltered_
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FIELDS nodalAtomicFieldsRoc_;
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FIELDS nodalAtomicFieldsRoc_;
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/*@}*/
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@ -740,9 +740,9 @@ namespace ATC {
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/** \name quadrature weights */
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//---------------------------------------------------------------
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/*@{*/
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DIAG_MAT NodeVolumes_;
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DIAG_MAN invNodeVolumes_;
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DIAG_MAT NodeVolumes_;
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DIAG_MAN invNodeVolumes_;
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/** atomic quadrature integration weights (V_\alpha) */
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ProtectedAtomDiagonalMatrix<double> * atomVolume_;
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std::string atomicWeightsFile_;
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@ -770,7 +770,7 @@ namespace ATC {
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bool needProcGhost_;
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std::string groupTag_;
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std::string groupTagGhost_;
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/** number of atoms of correct type,
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ghosts are atoms outside our domain of interest
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boundary are atoms contributing to boundary flux terms */
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@ -824,7 +824,7 @@ namespace ATC {
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SPAR_MAN kernelAccumulantMol_; // KKM add
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SPAR_MAN kernelAccumulantMolGrad_; // KKM add
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DIAG_MAN* accumulantWeights_;
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DIAG_MAN* accumulantInverseVolumes_;
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DIAG_MAN* accumulantInverseVolumes_;
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int accumulantBandwidth_;
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/*@}*/
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@ -845,7 +845,7 @@ namespace ATC {
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//---------------------------------------------------------------
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/** \name reference data */
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/** \name reference data */
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//---------------------------------------------------------------
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bool hasRefPE_;
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bool setRefPE_;
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